I haven't found explicit guidance, but enough that I can understand an agent getting heartburn. Deep in the bowels of Deltanet (knowledge management word search), I see this note in JS guidance:

"Note: Jumpseat riders are not permitted to activate as a nonrevenue passenger on the same flight where they have checked-in for the jumpseat."

Frankly, I don't even know what activate means. But if you have two listings and are only going to check in for one, that's problematic, right? Why have the other one... unless you're going to cancel after checking in and check in for the other listing? Or were you checking in for both, which obviously complicates the agent's job, who in this scenario was (possibly) busy trying to maximize butts in seats since you implied it was full?

Space available travel sucks, plain and simple. Sucks for those doing it and sucks for the agents trying to please their bosses with D0 perfection, NRSA and late/delayed/misconnect passengers running last-minute to catch the seat they paid for. I understand it's the job they signed up for, but I'm not sure you could pay me enough to do it day in and day out.